Function that performs pseudo-bulking on the data (VGM input), according to criteria specified by the User, and uses the pseudo-bulked data to perform Differential Gene Expression (DGE) analysis.

GEX_pseudobulk(
  vgm.input,
  column.group,
  group1,
  group2,
  column.comparison,
  comparison,
  pool,
  platypus.version
)

Arguments

vgm.input: Output of the VDJ_GEX_matrix function. Mandatory
column.group: Character vector. Mandatory. Column name of VDJ_GEX_matrix[[2]] where the groups to be tested for differenetial gene expression are located
group1: Strings vector. Mandatory. Samples to be grouped together for differential expression analysis against group2 (if pool=TRUE or column.comparison!=NULL). If pool=FALSE, vector containing samples to be tested individually against samples with the same index in the vector of group2.
group2: Strings vector. Mandatory. Samples to be grouped together for differential expression analysis against group1 (if pool=TRUE or column.comparison!=NULL). If pool=FALSE, vector containing samples to be tested individually against samples with the same index in the vector of group1.
column.comparison: Character vector. Defaults to NULL. Column name of VDJ_GEX_matrix[[2]] where the comparison cathegories are located, if DGE between group1 and group2 is performed across diferrent cathegories.
comparison,: Strings vector. Defaults to NULL. Comparison cathegories, if more than one is present.
pool: Logical. Defaults to FALSE. Indicates whether samples specified in group1 and group2 are to be pooled together within the same group.
platypus.version: This function works with "v3" only, there is no need to set this parameter

Value

A data.frame or list of data.frames containing the results of the DGE analysis for every level of pseudo-bulking.

Examples

if (FALSE) {
pseudo_DE<-GEX_pseudobulk(
vgm.input=VGM_NP396_GP33_GP66_labelled,
column.group="sample_id",
group1 = c("s1"), group2 = c("s4"),
column.comparison = "seurat_clusters",
comparison=c(2,3,5,9), pool=FALSE)
}